The effects of the combined treatments with aqueous chlorine dioxide (ClO2), fumaric acid and ultraviolet-C (UV-C) on the microbial quality of common buckwheat sprouts were examined using a response surface methodology. The populations of total aerobic bacteria, yeast and mould, and coliform decreased with increasing aqueous ClO2 and fumaric acid concentrations and increasing UV-C irradiation dose. However, the increase in the UV-C irradiation dose had a negative effect on the sensory quality. Therefore, the optimal combined treatment condition of 100 ppm aqueous ClO2, 0.31% fumaric acid and 1.9 kJ m−2 UV-C was selected for the buckwheat sprouts by providing reductions of 3.9, 1.8 and 2.4 log CFU g−1 on the populations of total aerobic bacteria, yeast and mould, and coliform, respectively. The combined treatment also maintained an acceptable sensory quality. These results suggest that the optimised combined treatment can be used as a microbial inactivation method for buckwheat sprouts.